8AEU | pdb_00008aeu

Structure of hMDM2 in complex with Nutlin-3a-aa

• PDB DOI: https://doi.org/10.2210/pdb8AEU/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-07-13 Released: 2023-01-18 
• Deposition Author(s): Labuzek, B., Golik, P., Magiera-Mularz, K., Berg, T.
• Funding Organization(s): Polish National Science Centre

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Nutlin-3a-aa: Improving the Bioactivity of a p53/MDM2 Interaction Inhibitor by Introducing a Solvent-Exposed Methylene Group.

Nietzold, F., Rubner, S., Labuzek, B., Golik, P., Surmiak, E., Del Corte, X., Kitel, R., Protzel, C., Reppich-Sacher, R., Stichel, J., Magiera-Mularz, K., Holak, T.A., Berg, T.

(2023) Chembiochem 24: e202300006-e202300006

• PubMed: 36602436 
• DOI: https://doi.org/10.1002/cbic.202300006
• Primary Citation Related Structures: 
  8AEU


• PubMed Abstract: 
  

  Nutlin-3a is a reversible inhibitor of the p53/MDM2 interaction. We have synthesized the derivative Nutlin-3a-aa bearing an additional exocyclic methylene group in the piperazinone moiety. Nutlin-3a-aa is more active than Nutlin-3a against purified wild-type MDM2, and is more effective at increasing p53 levels and releasing transcription of p53 target genes from MDM2-induced repression. X-ray analysis of wild-type MDM2-bound Nutlin-3a-aa indicated that the orientation of its modified piperazinone ring was altered in comparison to the piperazinone ring of MDM2-bound Nutlin-3a, with the exocyclic methylene group of Nutlin-3a-aa pointing away from the protein surface. Our data point to the introduction of exocyclic methylene groups as a useful approach by which to tailor the conformation of bioactive molecules for improved biological activity.

---

Organizational Affiliation: 
• Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany.
Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
Present address: Departamento de Química Orgánica I, Centro de Investigación y Estudios Avanzados "Lucio Lascaray", Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain.
Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.07 kDa 
• Atom Count: 777 
• Modeled Residue Count: 87 
• Deposited Residue Count: 97 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	97	Homo sapiens	Mutation(s): 0  EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0L (Subject of Investigation/LOI)	C [auth A]	4-[[(4~{S},5~{R})-4,5-bis(4-chlorophenyl)-2-(4-methoxy-2-propan-2-yloxy-phenyl)-4,5-dihydroimidazol-1-yl]carbonyl]-3-methylidene-piperazin-2-one C31 H30 Cl2 N4 O4 JLTUTZCZAIJXTD-WUFINQPMSA-N
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.233	α = 90
b = 56.233	β = 90
c = 75.376	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Labuzek, B., Golik, P., Magiera-Mularz, K., Berg, T.

---

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2014/12/W/NZ1/00457

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references
• Version 1.2: 2023-03-22
  Changes: Database references
• Version 1.3: 2023-03-29
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection, Refinement description